rs10490312

Positions:

• chr2-75290784-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739546.2(LOC107985900):​n.17918C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,262 control chromosomes in the GnomAD database, including 1,022 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (1022 hom., cov: 32)
• Consequence: LOC107985900 XR_001739546.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LOC107985900 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985900	XR_001739546.2	n.17918C>G		non_coding_transcript_exon_variant	1/2
LOC107985900	XR_001739545.2	n.17918C>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15841 AN: 152144 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.128

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.104 AC: 15853 AN: 152262 Hom.: 1022 Cov.: 32 AF XY: 0.101 AC XY: 7491 AN XY: 74440

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.00637

Gnomad4 SAS AF: 0.0603

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.125

Alfa AF: 0.119 Hom.: 147

Bravo AF: 0.102

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10490312; hg19: chr2-75517910;